Biology subjects

Rohatgi, R.

Publications and source records attributed to Rohatgi, R..

5 recordsLinked to original sources

bioRxiv2018

Bile Acid Biosynthesis Avoiding Cholesterol

Bile acids are the end products of cholesterol metabolism secreted into bile. They are essential for the absorption of lipids and lipid soluble compounds from the intestine. Here we have investigated the bile acid content of plasma and urine from patients with a defect in cholesterol biosynthesis, i.e. Smith-Lemli-Opitz syndrome (SLOS), resulting in elevated levels of 7-dehydrocholesterol (7-DHC), an immediate precursor of cholesterol. Using liquid chromatography - mass spectrometry (LC-MS) we have identified a novel pathway of bile acid biosynthesis in SLOS avoiding cholesterol starting with 7-DHC. This pathway also proceeds to a minor extent in healthy individuals. Monitoring of the pathway products could provide a rapid diagnostic for SLOS while elevated levels of pathway intermediates could be responsible for some of the features of the disease. Importantly, intermediates in the pathway are modulators of the activity of Smoothened, an oncoprotein that mediates Hedgehog signalling during embryogenesis and regeneration of postembryonic tissue.

biochemistry↗

bioRxiv2018

Cholesterol interaction sites on the transmembrane domain of the hedgehog signal transducer and Class F G protein-coupled receptor Smoothened

Transduction of hedgehog signals across the plasma membrane is a key process during animal development. This is facilitated by the Class F G-protein-coupled-receptor (GPCR) Smoothened (SMO), a major drug target in the treatment of basal cell carcinomas. Recent studies have suggested that SMO is modulated via interactions of its transmembrane (TM) domain with cholesterol. Long time scale (>0.35 ms of simulation time) molecular dynamics simulations of SMO embedded in two different cholesterol containing lipid bilayers reveal direct interactions of cholesterol with the transmembrane domain at regions distinct from those observed in Class A GPCRs. In particular the extracellular tips of helices TM2 and TM3 form a well-defined cholesterol interaction site, robust to changes in membrane composition and in force field parameters. Potential of mean force calculations for cholesterol interactions yield a free energy landscape for cholesterol binding. Combined with analysis of equilibrium cholesterol occupancy these results reveal the existence of a dynamic greasy patch interaction with the TM domain of SMO, which may be compared to previously identified lipid interaction sites on other membrane proteins. These predictions provide molecular level insights into cholesterol interactions with a biomedically relevant Class F GPCR, suggesting potential druggable sites.

biophysics↗

bioRxiv2018

Discovery of gene regulatory elements through a new bioinformatics analysis of haploid genetic screens

The systematic identification of regulatory elements that control gene expression remains a challenge. Genetic screens that use untargeted mutagenesis have the potential to identify protein-coding genes, non-coding RNAs and regulatory elements, but their analysis has mainly focused on identifying the former two. To identify regulatory elements, we conducted a new bioinformatics analysis of insertional mutagenesis screens interrogating WNT signaling in haploid human cells. We searched for specific patterns of retroviral gene trap integrations (used as mutagens in haploid screens) in short genomic intervals overlapping with introns and regions upstream of genes. We uncovered atypical patterns of gene trap insertions that were not predicted to disrupt coding sequences, but caused changes in the expression of two key regulators of WNT signaling, suggesting the presence of cis-regulatory elements. Our methodology extends the scope of haploid genetic screens by enabling the identification of regulatory elements that control gene expression.

bioinformatics↗

bioRxiv2018

Spatiotemporal manipulation of ciliary glutamylation reveals its roles in intraciliary trafficking and Hedgehog signaling

Tubulin post-translational modifications (PTMs) occur spatiotemporally throughout cells and are suggested to be involved in a wide range of cellular activities. However, the complexity and dynamic distribution of tubulin PTMs within cells have hindered the understanding of their physiological roles in specific subcellular compartments. Here we develop a method to rapidly deplete tubulin glutamlyation inside the primary cilia, a microtubule-based sensory organelle protruding on the cell surface, by targeting an engineered deglutamylase to the cilia in minutes. This rapid deglutamylation quickly leads to altered ciliary functions such as kinesin-2-mediated anterograde intraflagellar transport and Hedgehog signaling, along with no apparent crosstalk to other PTMs such as acetylation and detyrosination. Our study offers a feasible approach to spatiotemporally manipulate tubulin PTMs in living cells. Future expansion of the repertoire of actuators that regulate PTMs may facilitate a comprehensive understanding of how diverse tubulin PTMs encode ciliary as well as cellular functions.

cell biology↗

bioRxiv2017

R-spondins can potentiate WNT signaling without LGR receptors

The WNT signaling pathway regulates patterning and morphogenesis during embryonic development and promotes tissue renewal and regeneration in adults. Some WNT responses in vertebrates depend on a second signal provided by the R-spondin family of four secreted proteins (RSPO1-4) that drive the renewal of stem cells in many tissues. RSPOs markedly amplify target cell sensitivity to WNT ligands by neutralizing two transmembrane E3 ligases, ZNRF3 and RNF43, which reduce cell-surface levels of WNT receptors. Chromosomal translocations that increase RSPO expression or that inactivate ZNRF3/RNF43 can drive human cancers. RSPOs contain tandem furin-like repeats (FU1 and FU2), a thrombospondin type I (TSP) domain, and a basic region (BR). RSPOs simultaneously engage ZNRF3/RNF43 through their FU1 domain and one of three leucine-rich repeat-containing G-protein coupled receptors (LGR4-6) through their FU2 domain, triggering the clearance of ZNRF3/RNF43 and the consequent rise in WNT receptor levels. LGRs are selectively expressed in various tissue stem cells and are considered the primary high-affinity receptors for RSPOs. Using purified mutant and chimeric RSPOs and cell lines lacking various receptors, we show that RSPO2 and RSPO3, but not RSPO1 and RSPO4, can potentiate WNT/{beta}-catenin signaling in the absence of all three LGRs. The ZNRF3/RNF43-interacting FU1 domain was necessary for LGR-independent signaling, while the LGR-interacting FU2 domain was dispensable. The FU1 domain of RSPO3 was also sufficient to confer LGR-independence when transplanted to RSPO1, demonstrating that its interaction with ZNRF3/RNF43 dictates LGR-independent signaling. The enigmatic TSP/BR domains of RSPOs and their interaction with heparan sulfate proteoglycans (HSPGs), previously considered dispensable for WNT/{beta}-catenin signaling, became essential in the absence of LGRs. These results define two alternative modes of RSPO-mediated signaling that share a common dependence on ZNRF3/RNF43, but differ in their use of either LGRs or HSPGs, with implications for understanding their mechanism of action, biological functions and evolutionary origins.

developmental biology↗